Imam Ali al-Hadi (a.s.) made a decision to leave Medina for Samarra for the reason that Abd Allah ibn. Muhammad was put in charge of war and prayer in Medina, the city of the Apostle of Allah (s.a.w.). He told lies to Al-Mutawakkil with the intention of harming him. Imam al-Hadi (a.s.) learnt of his lying and wrote to al-Mutawakkil, mentioning ‘Abd Allah ibn Muhammad’s unfair treatment of him and the lies with which he had slandered him. Al-Mutawakkil sent his answer to his letter, in which he summoned him to come to al-‘Askar (Samarra) as an act of courtesy both in word and deed. The text of the letter has been preserved; it is:
"In the name of God, the Merciful, The Compassionate. . . The Commander of the faithful, being aware of your rank, caring for your close relationship (with him), judging matters which are appropriate for the circumstances of you and your House, confirms your dignity and their dignity, gives security to you and them, requiring by that the consent of his Lord and the performance of what is stipulated with regard to you and them.
The Commander of the faithful has been sent it as appropriate to dismiss ‘Abd Allah ibn Muhammad from his appointment over war and prayer in Medina, the city of the Apostle (s.a.w.), because he was ignorant of your rights, as you have mentioned, and took no account of your rank when he suspected you and attributed to you a matter in which the Commander of the faithful knew of your innocence, and of the truthfulness of your intentions through your piety and your words. You have not rendered yourself worthy when you suspected his (ex, the Commander of the faithful’s) request (to come to Samarra). The Commander of the faithful has appointed Muhammad bin. al-Fadl over what (the other man) used to administer. He has ordered him to honor and respect you, to carry out your orders and views and by that to be close to God and to the Commander of the faithful. However the Commander of the faithful is anxious to be close to you and to see you.
If you would come to visit him and reside with him as long as you want, then come, you and those whom you choose of your House, your retainers and your coterie, at your leisure and ease. You would travel when you wanted, stop when you wanted and go how you wanted. If you liked Yahya ibn. Harthama, the retainer of the Commander of the faithful, and the soldiers with him would travel with you and make the journey (with you). The decision about that is up to you. Ask God for a decision so that you may come to the Commander of the faithful. None of his brothers, his children, his family and his courtiers are as sympathetic to you as he is. No one is more praiseworthy in their treatment of you than him. No one among them is kinder to you, nor are any of them more respectful to you, nor more compassionate to you than he will be to you. Greetings and the mercy and blessings of God be on you."
Ibrahim ibn al-Abbas wrote (this letter) in the month of Jumada al-Akhira in the year 243 A.H. (857). When the letter reached Abu ul-Hasan (al-Hadi) [a.s.], he made preparations for the journey. Yahya ibn Harthama accompanied him until he reached Samarra. When he arrived there, al-Mutawakkil provided him with what was necessary at that time. He stayed in an inn called the Inn of al-Sa’alik. He resided there for a day. Then al-Mutawakkil gave him a house for himself and he moved there.
[Abu al-Qasim Jafar ibn Muhammad informed me on the authority of Muhammad ibn Ya’qub, on the authority of al-Hussein ibn Muhammad, on the authority of Mu’alla ibn Muhammad, on the authority of Ahmad ibn Muhammad ibn Abd Allah on the authority of Muhammad ibn Yahya on the authority of Salih ibn Sa’id, who said:]
"I (i.e. Salih ibn Said) visited Abu al-Hassan (al-Hadi) [a.s.], on the day of his coming to Samarra. I said to him: "May I be your ransom, in every matter they are only concerned to extinguish your light and to diminish you so that they have put you to stay in this hideous inn - the Inn of al-Sa’alik."
"Here you are Ibn Sa’id," he said, and indicated with his hand. Suddenly I was amid pleasant gardens and flowing rivers and gardens in which were perfumed plants and beautiful maidens like veiled pearls. My sight became confused and my amazement was great. He said to me: "This is where we are. This belongs to us, Ibn Sa’id. WE are not in the Inn of al-Sa’alik."
Abu al-Hassan (al-Hadi) [a.s.], resided for a time at his residence in Samarra publicly honored. Yet al-Mutawakkil endeavored to make him fall into a trap but he was not able to do that. The reports of him with (al-Mutawakkil) in which there are signs and indications of his (Imamate) are so numerous that it would make the book too long to mention them. If we attempted to present them, we would have to abandon the purpose we set for ourselves.
Abu al-Hassan (a.s.) died in Rajab in the year 254 A.H. (868) in his house in Samarra. Among the children he left behind is Abu-Muhammad al-Hassan, his son who was the Imam after him, al-Hussein, Muhammad, Ja’far and his daughter, A’isha. He resided in Samarra for ten years and some months until his death. He died at the age of forty-one.

Reference: Shaykh al-Mufid. Kitab Al-Irshad (The Book of Guidance). Islamic Republic of Iran. Pages 504-506.